L1kdeconv: an R package for peak calling analysis with LINCS L1000 data.

ABSTRACT:

Background

LINCS L1000 is a high-throughput technology that allows gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every two landmark genes are designed to share a single channel. Thus, a deconvolution step is required to infer the expression values of each gene. Any errors in this step can be propagated adversely to the downstream analyses.

Results

We presented a LINCS L1000 data peak calling R package l1kdeconv based on a new outlier detection method and an aggregate Gaussian mixture model (AGMM). Upon the remove of outliers and the borrowing information among similar samples, l1kdeconv showed more stable and better performance than methods commonly used in LINCS L1000 data

SUBMITTER: Li Z 

PROVIDER: S-EPMC5532784 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature